[Freesurfer] subcortical brain intensity
HI all What is mean of the subcortical intensity in the aseg.stats file? Thanks. rujing___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to convert fsaverage space mask into other subject original space
Hi Bruce and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha At 2014-04-08 23:10:35,Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what kind of a mask? If a label you can use mri_label2label cheers Bruce On Tue, 8 Apr 2014, Rujing Zha wrote: Hi FS experts and others, I try to check my group analysis result by seeing the subjects' original space corresponding area. So I need to know how to convert my mask from fsaverage space into specific subject's space. Thanks All the best. RujingZha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fw:Re: Re: questions about ROI analysis
Hi FS experts and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha 转发邮件信息 发件人：charujing123 charujing...@163.com 发送日期：2014-02-27 09:46:23 收件人：freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu 主题：Re: Re: [Freesurfer] questions about ROI analysis Thanks doug, All the best. Rujing Zha 2014-02-27 charujing123 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-02-27 01:49 主题：Re: [Freesurfer] questions about ROI analysis 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： On 02/25/2014 08:34 PM, charujing123 wrote: Hidoug, Thanks doug. For 1st question,I want to reduce the search space of vertex-wise analysis to a cluster. Extract the cluster that you want from the ocn to create a mask, eg, to get cluster2 mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh The run mri_glmfit with --mask cluster2.mgh Then run mri_glmfit-sim with simulation For 2nd question, i try freeview as tksurfer cannot work. However this website cannot be logged in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit. try http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide Thanks. All the best. Rujing Zha 2014-02-26 charujing123 *发件人：*Douglas Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-02-25 23:46 *主题：*Re: [Freesurfer] questions about ROI analysis *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄送：* On 2/25/14 10:09 AM, Rujing Zha wrote: Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim? Do you mean you want to reduce the search space of a vertex-wise analysis to a cluster or that you want to compute the mean thickness within the cluster and correlate with your behavioral score? 2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask. tksurfer can draw a label (as can freeview I think) Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom
[Freesurfer] questions about ROI analysis
Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim? 2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask. Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freeview error {Disarmed}
Dear Ruopeng, Thanks for your help, Ruopeng.I learned the groupanalysis by manu ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this command on your tutorial data (buckner data). Would you please tell me where my hardware setup is inappropriate? Thanks. All the best. Rujing Zha Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2014-01-03 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: freeview error
Dear Ruopeng, Thanks for your help, Ruopeng.I learned the groupanalysis by manu of http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this command on your tutorial data (buckner data). Would you please tell me where my hardware setup is inappropriate? Thanks. All the best. 2014-01-01 Rujing Zha 发件人：Ruopeng Wang rpw...@nmr.mgh.harvard.edu 发送时间：2014-01-01 00:16 主题：Re: [Freesurfer] Fwd: freeview error 收件人：rujing chacharuj...@gmail.com 抄送：charujing123charujing...@163.com,freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, Your hardware setup does sound a bit insufficient to run freeview smoothly. But I don't think that is the reason configure overlay hangs. Would it be possible to send us the files used in your command? Best, Ruopeng On Dec 31, 2013, at 1:04 AM, rujing cha charuj...@gmail.com wrote: Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freeview error
Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freeview error
Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] reconall error
Dear Bruce and others, As my server has a bad graphic card, so I want to install freesurfer in my computer. My computer can support OpenGL, and I installed ubuntu as I didnot know how to setup the graphic card driver in CentOS(I didnot know whether it was needed to setup). I completed the freeesurfer license and configured the bashrc. Then I ran the freesurfer command, such as freeview, but it told me that permission denied. So I chmod 777 -R freesurfer, but it still told me permission denied. My system is ubuntu1310desktopamd64. Bruce, or others, would you please help me? All what I have done is to visualize the overlay,underlay and annotation in freeview but my server cannot do that. Thanks. All the best. 2013-12-27 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-10-31 03:58 主题：Re: [Freesurfer] reconall error 收件人：Rashmi Singhrsi...@laureateinstitute.org 抄送：freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Hi Rashmi can you try 5.3 and see if it works? Alternatively you can email me the orig.mgz and I can try it Bruce On Wed, 30 Oct 2013, Rashmi Singh wrote: Hey Bruce, I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check flags) with a data set that failed showing the same error that I had received earlier. I am sure have the correct data set. I am attaching the recon-all.log and the data. We have FreeSurfer Version 5.1.0 Please advice. Thanks, Rashmi On 10/23/13 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi what version are you running? If 5.3, upload the subject and I'll take a look Bruce On Tue, 22 Oct 2013, Rashmi Singh wrote: Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T 2Practice/FreeSurfer/AA470-2prac/ mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as 20.2 or 943.7 total sample mean = 92.0 (1443 zeros) spacing=8, using 3481 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 -- 126 resetting gm mean[0]: 74 -- 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) -- (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) -- (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org
Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit
Hi Gari, Thanks for your helpful prompt. I see. All the best. 2013-12-21 Rujing Zha 发件人：Garikoitz Lerma-Usabiaga gariko...@gmail.com 发送时间：2013-12-21 15:47 主题：Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, About tksurfer visualization, we had the same problem, it was because the graphic card in the server, you cannot do anything about it (well, install a different one). If I remember correctly, you need a graphic card that supports OpenGL. Regards, Gari On Friday, December 20, 2013, Rujing Zha wrote: Thanks Doug. All the best. 2013-12-20 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-20 00:14 主题：Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit 收件人：Rujing Zhazh...@mail.ustc.edu.cn,Bruce Fischlfis...@nmr.mgh.harvard.edu 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu On 12/19/2013 07:22 AM, Rujing Zha wrote: Hi Doug, Bruce and others. Would you please help me deal with 2 problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz(i.e. picture 2 in the attachment),but neither did -aseg image which had those voxels(i.e. picture 1 in the attachment) which I have removed from the brainmask.mgz when I ran tkmedit subject brainmask.mgz -aux wm.mgz -surfs -aseg. Does this incorrect aseg image will influence my group thickness analysis? If so, what can I do to fix it? I don't think you need to fix that. It is dura but it does not look like it is affecting the surfaces. The cortical segmentation in the aseg is not that important since all cortical statistics are computed from the cortical surfaces, not the aseg. The 2nd one is : I could not visualize the inflated image properly in tksurfer by this command: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I visualized the inflated image in the freeview tool by typing freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated . The result can be seen in picture 5. I don't know, looks like a problem with the libraries needed for display. Maybe Zeke or Ruopeng can weight in. CentOS 5.8 is used in my server and I use freesurfer-Linux-centos4-stable-pib-v5.3.0. Thanks in advance. All the best. 2013-12-17 /Rujing Zha/ School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn mailto:zh...@mail.ustc.edu.cn charuj...@gmail.com mailto:charuj...@gmail.com charujing...@163.com mailto:charujing...@163.com *发件人：*Bruce Fischl fis...@nmr.mgh.harvard.edu *发送时间：*2013-12-16 23:57 *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件人：*Rujing Zhacharujing...@163.com *抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] vertex-wise threshold and cluster-wise p values
Hi all, I want to know difference between vertex-wise and cluster-wise in Groupanalysis. Can I just think vertex-wise are uncorrected P-value(which is the same as voxel-wise value) and cluster-wise value are the vertex population which are survived after a specific threshold correction? Thanks. All the best. 2013-12-21 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] p value in CWP colume
Hi all, I just study group analysis tutorial and I am confused with how to find cluster-wise probability in CWP colume(i.e 0.2 in clusterno 1). Did I need to process additinoally? Thanks. All the best. 2013-12-21 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com attachment: attachment.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Doug,
Doug, it's very kind of you to help me all the time. Thanks.
I didnot do anything except move all DICOM files into one folder which is the
same as other subjects. According your prompt, I checked the DICOM and found
that this subjects have two 3d imag. And I separated the data into 2 folders.
So the recon-all running normally.
Thanks Doug.
All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 04:48
主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the
command-line ERROR
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
There are lots of warnings in the log file. Have you anonymized this
data or done anything to the DICOM files since they came from the scanner?
On 12/18/2013 03:44 AM, Rujing Zha wrote:
Dear Doug,
Thanks for your kindhearted help, Doug.
I upload the standard output and error message file named
unpack_log, and the unpack log file named unpack.log in the attachment.
Thanks in advance.
All the best.
2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-18 00:51
*主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from
the command-line ERROR
*收件人：*Rujing Zhacharujing...@163.com
*抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu
Is that all it says? Can you send the log file?
On 12/16/2013 10:00 PM, Rujing Zha wrote:
Hi Doug,
Thanks Doug.
I tried the -run 15 option, it generate a 015 folder. However
unpacksdcmdir code echo ERROR message:
ERROR:mri_convert
child killed: segmentation violation ,
and the script terminated.
All the best.
2013-12-17
/Rujing Zha/
*发件 人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-17 02:56
*主 题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from
the command-line ERROR
*收件 人：*freesurferfreesurfer@nmr.mgh.harvard.edu
*抄送：*
If you passed -run 015 it should have generated a 015 folder and not a
013 folder. The only thing I can think may have gone wrong is that it
expected 15 instead of 015.
doug
On 12/16/2013 09:24 AM, Bruce Fischl wrote:
sorry, I don't know that code very well. Doug is probably the right
one to help you
Bruce
On Mon, 16 Dec 2013, Rujing Zha wrote:
Dear Bruce,
I did setup the -run 015 not 013 in unpacksdcmdir as I told in
previous
message. But it generated the 013 folder automatically after running
unpacksdcdir, which made me so confused.
As it created the 013 folder, I guess unpacksdcmdir didnot recognized
structure image correctly which was in the 15th line of the scan.info.
Thanks Bruce.
All the best.
2013-12-16
Rujing Zha
发 件 人：Bruce Fischl fis...@nmr.mgh.harvard.edu
发送时间：2013-12-16 22:12
主
题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the
command-line ERROR
收件 人：Rujing Zhacharujing...@163.com
抄 送：freesurferfreesurfer@nmr.mgh.harvard.edu
but why are you giving recon-all the path to run 013 instead of 015? I
don't know the fsfast file structure, but your scan.info says that
013 is
?? ?an EPI fun and 015 is the mprage
On Sat,
14 Dec 2013, Rujing Zha wrote:
Hi Bruce,
It generated a 013 subfolder in after running this code unpacksdcmdir
-src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015
3danat mg
z
001.mgz. It is 15 that I can see the number of
t1_mpr_ns_sag_iso_zhang
?? ?in
the unpack.log.
Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s
liujunha
o,
and it finished without error.
recon-all -s liujunhao -all was run and ERROR would be displayed:
ERROR: input(s) cannot have multiple frames!
The recon-all.log unpack.log and scan.info were unloaded in the
attachmen
t.
Thanks.
All the best.
2013-12-14
_
___
Rujing Zha
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Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc
Hi Doug,
I just found the module.
All the best.
2013-12-19
Rujing Zha
发件人：Rujing Zhacharujing...@163.com
发送时间：2013-12-19 15:02
主题：Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after
mris_preproc
收件人：Douglas N Grevegr...@nmr.mgh.harvard.edu
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
Hi Doug,
Doug, thanks for your attention.
When I type the command as described detaily in picture 3 in the attachment
which is similar to
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=2,5
. It represented picture 1 at the beginning and then picture 2 was
represented. Picture 1 and 2 also can be got in the attachment. Then I want to
click Show outline only, but I cannot find the module in freeview. And I had
no idea about Once the aparc parcellation appears on the inflated surface.
Thanks.
All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 04:38
主题：Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after
mris_preproc
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
I don't know what you mean. Can you elaborate?
doug
On 12/17/2013 10:12 PM, Rujing Zha wrote:
Dear Doug,
Thanks Doug.
In my server, I cannot visualize the file but seeing the time courese
window. I want to know whether there is a limit in graphics card for
visualing the inflated data.
Thanks.
All the best.
2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-18 00:32
*主题：*Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh
after mris_preproc
*收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
*抄送：*
You can load is as an overlay in tksurfer or freeview and scroll through
the frames
On 12/17/2013 07:21 AM, Rujing Zha wrote:
Dear all,
I read the tutorial
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
and I want to know how to visualize the lh.gender_age.thickness.10.mgh.
Thanks.
All the best.
2013-12-17
/Rujing Zha/
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_glmfit error
Hi Doug and others,
Thanks Doug.
All the best.
2013-12-20
Rujing Zha
发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-20 00:11
主题：Re: [Freesurfer] mri_glmfit error
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
On 12/18/2013 11:14 PM, Rujing Zha wrote:
Hi Doug and others,
Thanks Doug.
For the 2nd problem: I understand orthogonalization between nuisance
variables. I just want to test the difference between two group mean
pial thickness controling the age and edu (if it is necessary to
control the age and sex). So I guess I have two option: one: I can
select one of them discarding the other one in the fsgd. the other
one: I select both of them, and ignoring the high correlation.
For the 3rd problem: As I just want to know the difference between 2
group pial thickness controling some other factors which may explain
my result, so I guess I just donot consider the sex as a nuisance factor.
Is that appropriate?
I don't know. It is not a question for me to answer since it depends on
the data.
There is a new problem for me:
I also want to do a partial analysis between pial thickness analysis
and behavior score. The numbers of class in fsgd file are the same as
this one except adding another colume for the score. Is this correct?
Yes
Thanks.
All the best.
2013-12-19
/Rujing Zha/
*发件人：*Douglas Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-19 11:34
*主题：*Re: [Freesurfer] mri_glmfit error
*收件人：*Rujing Zhacharujing...@163.com
*抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu
On 12/18/13 10:26 PM, Rujing Zha wrote:
Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the
attachment.
And I am confused with 3 problems:
1st: Is what I modified proper?
Yes
2nd: How can I deal with my high correlation between age and edu?
If they are nuisance variables, then you could orthogonalize one with
respect to the other. If you really want to test for a difference in
groups for the age slope or the edu slope, then there is nothing you
can do except get more subjects.
3rd: Is it necessary to tell mri_glmfit to distinguish which subject
is female or male in each class if dividing all subjects into 2
classes (i.e con and IA )?
If you only have con and IA, you cannot have a gender factor. If you
think that a gender factor is really necessary, then you need to get
more females.
doug
Thanks in advance.
All the best.
2013-12-19
/Rujing Zha/
*发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-19 04:59
*主题：*Re: [Freesurfer] mri_glmfit error
*收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
*抄送：*
Could be several things. You only have two IA_female and and only 3
con_female. Also, the age and edu are highly correlated. I would try
creating a single IA group with males and females and a single con group
doug
On 12/18/2013 11:21 AM, Rujing Zha wrote:
Hi all,
I try to run mri_glmfit, but it export
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class..
I upload the data in the attachment, and the glmfit_output is the
standard output of the mri_glmfit.
Thanks.
All the best.
2013-12-19
/Rujing Zha/
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender and
properly
Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit
Thanks Doug. All the best. 2013-12-20 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-20 00:14 主题：Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit 收件人：Rujing Zhazh...@mail.ustc.edu.cn,Bruce Fischlfis...@nmr.mgh.harvard.edu 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu On 12/19/2013 07:22 AM, Rujing Zha wrote: Hi Doug, Bruce and others. Would you please help me deal with 2 problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz(i.e. picture 2 in the attachment),but neither did -aseg image which had those voxels(i.e. picture 1 in the attachment) which I have removed from the brainmask.mgz when I ran tkmedit subject brainmask.mgz -aux wm.mgz -surfs -aseg. Does this incorrect aseg image will influence my group thickness analysis? If so, what can I do to fix it? I don't think you need to fix that. It is dura but it does not look like it is affecting the surfaces. The cortical segmentation in the aseg is not that important since all cortical statistics are computed from the cortical surfaces, not the aseg. The 2nd one is : I could not visualize the inflated image properly in tksurfer by this command: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I visualized the inflated image in the freeview tool by typing freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated . The result can be seen in picture 5. I don't know, looks like a problem with the libraries needed for display. Maybe Zeke or Ruopeng can weight in. CentOS 5.8 is used in my server and I use freesurfer-Linux-centos4-stable-pib-v5.3.0. Thanks in advance. All the best. 2013-12-17 /Rujing Zha/ School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn mailto:zh...@mail.ustc.edu.cn charuj...@gmail.com mailto:charuj...@gmail.com charujing...@163.com mailto:charujing...@163.com *发件人：*Bruce Fischl fis...@nmr.mgh.harvard.edu *发送时间：*2013-12-16 23:57 *主题：*Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR *收件人：*Rujing Zhacharujing...@163.com *抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Hi Bruce, Maybe 163 email has some problems. I will try my gmail to send you and Louis my data. But I donot know whether your email can get attachment size 289M? Thanks. All the best. 2013-12-16 Rujing Zha 发件 人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:37 主 题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件 人：Rujing Zhacharujing...@163.com 抄 送：freesurferfreesurfer@nmr.mgh.harvard.edu no, I didn't get it On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 _ ___ Rujing Zha _ ___ 发件 人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主 题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ? command-line ERROR 收件 人：Rujing Zhacharujing...@163.com 抄 送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one t o ?? ? help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in prev io us message. But it generated the 013 folder automatically after running ?? ? unpacksdcdir, which made me so confused. As it created the 013
[Freesurfer] tcsh in groupanalysis
Hi all, I learned the tutorial in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis;. At the beginning of the manu, it told me to run command in tcsh. Can I just run commands in bash shell. If so, what is the function of tcsh? Thanks. All the best. 2013-12-18 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit error
Hi all, I try to run mri_glmfit, but it export ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.. I upload the data in the attachment, and the glmfit_output is the standard output of the mri_glmfit. Thanks. All the best. 2013-12-19 Rujing Zha age_edu.fsgd Description: Binary data glmfit_output Description: Binary data lh-Diff-con-IA-Intercept-thickness.mtx Description: Binary data mri_glmfit.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] design matrix and contrast in fsgdf
Hi Doug,
OK, I see. Thanks Doug.
All the best.
2013-12-19
Rujing Zha
发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 04:38
主题：Re: [Freesurfer] design matrix and contrast in fsgdf
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
yes
On 12/17/2013 10:06 PM, Rujing Zha wrote:
Dear Doug,
Thanks for your precious help.
Considering the 2nd example, I just want to know whether some brain
surface thickness correlate the score without subjects coming from
control or patient group. I think my aim is the same as want you told
me test whether the score is equal to 0 or not. Am I right?
Thanks.
All the best.
2013-12-18
/Rujing Zha/
*发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-18 00:31
*主题：*Re: [Freesurfer] design matrix and contrast in fsgdf
*收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
*抄送：*
That looks correct. The contrasts for the 2nd example will test whether
the score is equal to 0 or not (and not an interaction between diagnosis
and score). It is not wrong, but I just wanted to make sure you know
what you are testing.
doug
On 12/17/2013 01:50 AM, Rujing Zha wrote:
Dear all,
I want to design a group t-test analysis and correlation analysis for
pial thickness. I have read the PPT of freesurfer.groupanalysis, and I
wrote a specific design matrix and contrast for my data. However it is
the first time that I design matrix in fsgdf by freesurfer. I didnot
confirm whether I wrote is correct. I need someone to help me review it.
I have two groups, four groups were classified as sex.(Is this
necessary or correct?)
Here is my design matrix in fsgdf for 2 group t-test:
GroupDescriptorFile 1
Title lh_ttest
Class con_male
Class con_female
Class pat_male
Class pat_female
Variables Age edu
Input subjid1 con_male 19 10
Input subjid2 con_male 20 20
Input subjid3 con_male 20 20
Input subjid4 con_male 19 10
Input subjid5 con_female 20 20
Input subjid6 con_female 20 20
Input subjid7 con_female 19 10
Input subjid8 pat_male 20 20
Input subjid9 pat_male 20 20
Input subjid10 pat_male 19 10
Input subjid11 pat_female 20 20
Input subjid12 pat_female 20 20
DefaultVariable Age
In this section, I just want to compare the patient group(class 3 and
4) and control group(class 1 and 2) in thickness controling the age
and education by ANCOVA. Does this fsgdf implement ANCOVA?
Here is my contrast for this:
0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0
Here is my design matrix in fsgdf for partial regression:
GroupDescriptorFile 1
Title lh_regression
Class con_male
Class con_female
Class pat_male
Class pat_female
Variables Age edu score1 score2
Input subjid1 con_male 19 10 20 30
Input subjid2 con_male 20 20 20 30
Input subjid3 con_male 20 20 20 30
Input subjid4 con_male 19 10 20 30
Input subjid5 con_female 20 20 20 30
Input subjid6 con_female 20 20 20 30
Input subjid7 con_female 19 10 20 30
Input subjid8 pat_male 20 20 20 30
Input subjid9 pat_male 20 20 20 30
Input subjid10 pat_male 19 10 20 30
Input subjid11 pat_female 20 20 20 30
Input subjid12 pat_female 20 20 20 30
DefaultVariable score1
In this section, I want to implement partial regression analysis(i.e.
score1 and score2) by controling the age,edu and sex.
Here is my contrast for score1:
0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0
Here is my contrast for score2:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25
Any reply will be highly appreciated.
Thanks.
All the best.
2013-12-17
/Rujing Zha/
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] tcsh in groupanalysis
Hi Doug, I see. Thanks Doug. All the best. 2013-12-19 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-19 04:49 主题：Re: [Freesurfer] tcsh in groupanalysis 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： You do not, but you will need to source the proper env file ( SetUpFreeSurfer.sh instead of SetUpFreeSurfer.csh) doug On 12/18/2013 09:57 AM, Rujing Zha wrote: Hi all, I learned the tutorial in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis;. At the beginning of the manu, it told me to run command in tcsh. Can I just run commands in bash shell. If so, what is the function of tcsh? Thanks. All the best. 2013-12-18 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_glmfit error
Hi Doug and others, Thanks Doug. I modifiled my number of class in the fsgd which can be got in the attachment. And I am confused with 3 problems: 1st: Is what I modified proper? 2nd: How can I deal with my high correlation between age and edu? 3rd: Is it necessary to tell mri_glmfit to distinguish which subject is female or male in each class if dividing all subjects into 2 classes (i.e con and IA )? Thanks in advance. All the best. 2013-12-19 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-19 04:59 主题：Re: [Freesurfer] mri_glmfit error 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Could be several things. You only have two IA_female and and only 3 con_female. Also, the age and edu are highly correlated. I would try creating a single IA group with males and females and a single con group doug On 12/18/2013 11:21 AM, Rujing Zha wrote: Hi all, I try to run mri_glmfit, but it export ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.. I upload the data in the attachment, and the glmfit_output is the standard output of the mri_glmfit. Thanks. All the best. 2013-12-19 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. age_edu.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_glmfit error
Hi Doug and others, Thanks Doug. For the 2nd problem: I understand orthogonalization between nuisance variables. I just want to test the difference between two group mean pial thickness controling the age and edu (if it is necessary to control the age and sex). So I guess I have two option: one: I can select one of them discarding the other one in the fsgd. the other one: I select both of them, and ignoring the high correlation. For the 3rd problem: As I just want to know the difference between 2 group pial thickness controling some other factors which may explain my result, so I guess I just donot consider the sex as a nuisance factor. Is that appropriate? There is a new problem for me: I also want to do a partial analysis between pial thickness analysis and behavior score. The numbers of class in fsgd file are the same as this one except adding another colume for the score. Is this correct? Thanks. All the best. 2013-12-19 Rujing Zha 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-19 11:34 主题：Re: [Freesurfer] mri_glmfit error 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu On 12/18/13 10:26 PM, Rujing Zha wrote: Hi Doug and others, Thanks Doug. I modifiled my number of class in the fsgd which can be got in the attachment. And I am confused with 3 problems: 1st: Is what I modified proper? Yes 2nd: How can I deal with my high correlation between age and edu? If they are nuisance variables, then you could orthogonalize one with respect to the other. If you really want to test for a difference in groups for the age slope or the edu slope, then there is nothing you can do except get more subjects. 3rd: Is it necessary to tell mri_glmfit to distinguish which subject is female or male in each class if dividing all subjects into 2 classes (i.e con and IA )? If you only have con and IA, you cannot have a gender factor. If you think that a gender factor is really necessary, then you need to get more females. doug Thanks in advance. All the best. 2013-12-19 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-19 04:59 主题：Re: [Freesurfer] mri_glmfit error 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Could be several things. You only have two IA_female and and only 3 con_female. Also, the age and edu are highly correlated. I would try creating a single IA group with males and females and a single con group doug On 12/18/2013 11:21 AM, Rujing Zha wrote: Hi all, I try to run mri_glmfit, but it export ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.. I upload the data in the attachment, and the glmfit_output is the standard output of the mri_glmfit. Thanks. All the best. 2013-12-19 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc
Dear all, I read the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and I want to know how to visualize the lh.gender_age.thickness.10.mgh. Thanks. All the best. 2013-12-17 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] data uploaded
Hi Bruce, I uploaded the data to your server. All files can be divided into 2 subjects. And one subject has incorrect segmentation (subject), the other has a multiframe ERROR(LJH_error). Thanks. All the best. 2013-12-17 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] design matrix and contrast in fsgdf
Dear Doug, Thanks for your precious help. Considering the 2nd example, I just want to know whether some brain surface thickness correlate the score without subjects coming from control or patient group. I think my aim is the same as want you told me test whether the score is equal to 0 or not. Am I right? Thanks. All the best. 2013-12-18 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-18 00:31 主题：Re: [Freesurfer] design matrix and contrast in fsgdf 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： That looks correct. The contrasts for the 2nd example will test whether the score is equal to 0 or not (and not an interaction between diagnosis and score). It is not wrong, but I just wanted to make sure you know what you are testing. doug On 12/17/2013 01:50 AM, Rujing Zha wrote: Dear all, I want to design a group t-test analysis and correlation analysis for pial thickness. I have read the PPT of freesurfer.groupanalysis, and I wrote a specific design matrix and contrast for my data. However it is the first time that I design matrix in fsgdf by freesurfer. I didnot confirm whether I wrote is correct. I need someone to help me review it. I have two groups, four groups were classified as sex.(Is this necessary or correct?) Here is my design matrix in fsgdf for 2 group t-test: GroupDescriptorFile 1 Title lh_ttest Class con_male Class con_female Class pat_male Class pat_female Variables Age edu Input subjid1 con_male 19 10 Input subjid2 con_male 20 20 Input subjid3 con_male 20 20 Input subjid4 con_male 19 10 Input subjid5 con_female 20 20 Input subjid6 con_female 20 20 Input subjid7 con_female 19 10 Input subjid8 pat_male 20 20 Input subjid9 pat_male 20 20 Input subjid10 pat_male 19 10 Input subjid11 pat_female 20 20 Input subjid12 pat_female 20 20 DefaultVariable Age In this section, I just want to compare the patient group(class 3 and 4) and control group(class 1 and 2) in thickness controling the age and education by ANCOVA. Does this fsgdf implement ANCOVA? Here is my contrast for this: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Here is my design matrix in fsgdf for partial regression: GroupDescriptorFile 1 Title lh_regression Class con_male Class con_female Class pat_male Class pat_female Variables Age edu score1 score2 Input subjid1 con_male 19 10 20 30 Input subjid2 con_male 20 20 20 30 Input subjid3 con_male 20 20 20 30 Input subjid4 con_male 19 10 20 30 Input subjid5 con_female 20 20 20 30 Input subjid6 con_female 20 20 20 30 Input subjid7 con_female 19 10 20 30 Input subjid8 pat_male 20 20 20 30 Input subjid9 pat_male 20 20 20 30 Input subjid10 pat_male 19 10 20 30 Input subjid11 pat_female 20 20 20 30 Input subjid12 pat_female 20 20 20 30 DefaultVariable score1 In this section, I want to implement partial regression analysis(i.e. score1 and score2) by controling the age,edu and sex. Here is my contrast for score1: 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 Here is my contrast for score2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 Any reply will be highly appreciated. Thanks. All the best. 2013-12-17 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information
Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc
Dear Doug, Thanks Doug. In my server, I cannot visualize the file but seeing the time courese window. I want to know whether there is a limit in graphics card for visualing the inflated data. Thanks. All the best. 2013-12-18 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-18 00:32 主题：Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： You can load is as an overlay in tksurfer or freeview and scroll through the frames On 12/17/2013 07:21 AM, Rujing Zha wrote: Dear all, I read the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and I want to know how to visualize the lh.gender_age.thickness.10.mgh. Thanks. All the best. 2013-12-17 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Bruce, I saw the scan.info, and the 13 line is functional image which has a 6 number. I guess this is why recon-all report the multiple frames. Would you please tell me how I can deal with this problem which unpacksdcmdir recognize the number 13 not 15? Thanks. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 21:54 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing why does the input volume have multiple frames? Is it a multi-echo dataset? cheers Bruce On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 Rujing Zha The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mgz 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunhao, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachment. Thanks. All the best. 2013-12-14 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Bruce, Maybe 163 email has some problems. I will try my gmail to send you and Louis my data. But I donot know whether your email can get attachment size 289M? Thanks. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:37 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu no, I didn't get it On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks Bruce. That's all right. I want to know if I e-mail to you my subject's data successfully. The subject's image had a incorrect segmentation in surfs after recon-all. Thanks in advance. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:24 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, I don't know that code very well. Doug is probably the right one to ?? ? help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previo us message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. ?? ? Thanks Bruce. All the best. 2013-12-16 _ ___ Rujing Zha _ ___ 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ? command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I ?? ? don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir ?? ? -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat ?? ?mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhan g ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujun ha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachm en t. Thanks. All the best. 2013-12-14 ___ __ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e- ma il contains patient information, please contact the Partners Compliance Help Li ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and p ro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners
Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR
Hi Doug, Thanks Doug. I tried the -run 15 option, it generate a 015 folder. However unpacksdcmdir code echo ERROR message: ERROR:mri_convert child killed: segmentation violation , and the script terminated. All the best. 2013-12-17 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-17 02:56 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： If you passed -run 015 it should have generated a 015 folder and not a 013 folder. The only thing I can think may have gone wrong is that it expected 15 instead of 015. doug On 12/16/2013 09:24 AM, Bruce Fischl wrote: sorry, I don't know that code very well. Doug is probably the right one to help you Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: Dear Bruce, I did setup the -run 015 not 013 in unpacksdcmdir as I told in previous message. But it generated the 013 folder automatically after running unpacksdcdir, which made me so confused. As it created the 013 folder, I guess unpacksdcmdir didnot recognized structure image correctly which was in the 15th line of the scan.info. Thanks Bruce. All the best. 2013-12-16 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-16 22:12 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu but why are you giving recon-all the path to run 013 instead of 015? I don't know the fsfast file structure, but your scan.info says that 013 is ?? ?an EPI fun and 015 is the mprage On Sat, 14 Dec 2013, Rujing Zha wrote: Hi Bruce, It generated a 013 subfolder in after running this code unpacksdcmdir -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3danat mg z 001.mgz. It is 15 that I can see the number of t1_mpr_ns_sag_iso_zhang ?? ?in the unpack.log. Then I ran recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liujunha o, and it finished without error. recon-all -s liujunhao -all was run and ERROR would be displayed: ERROR: input(s) cannot have multiple frames! The recon-all.log unpack.log and scan.info were unloaded in the attachmen t. Thanks. All the best. 2013-12-14 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] design matrix and contrast in fsgdf
Dear all, I want to design a group t-test analysis and correlation analysis for pial thickness. I have read the PPT of freesurfer.groupanalysis, and I wrote a specific design matrix and contrast for my data. However it is the first time that I design matrix in fsgdf by freesurfer. I didnot confirm whether I wrote is correct. I need someone to help me review it. I have two groups, four groups were classified as sex.(Is this necessary or correct?) Here is my design matrix in fsgdf for 2 group t-test: GroupDescriptorFile 1 Title lh_ttest Class con_male Class con_female Class pat_male Class pat_female Variables Ageedu Input subjid1 con_male 1910 Input subjid2 con_male 2020 Input subjid3 con_male 2020 Input subjid4 con_male 1910 Input subjid5 con_female 20 20 Input subjid6 con_female 2020 Input subjid7 con_female 1910 Input subjid8 pat_male 2020 Input subjid9 pat_male 2020 Input subjid10 pat_male 1910 Input subjid11 pat_female 2020 Input subjid12 pat_female 2020 DefaultVariable Age In this section, I just want to compare the patient group(class 3 and 4) and control group(class 1 and 2) in thickness controling the age and education by ANCOVA. Does this fsgdf implement ANCOVA? Here is my contrast for this: 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Here is my design matrix in fsgdf for partial regression: GroupDescriptorFile 1 Title lh_regression Class con_male Class con_female Class pat_male Class pat_female Variables Ageedu score1 score2 Input subjid1 con_male 1910 2030 Input subjid2 con_male 2020 2030 Input subjid3 con_male 2020 2030 Input subjid4 con_male 1910 2030 Input subjid5 con_female 20 20 2030 Input subjid6 con_female 2020 2030 Input subjid7 con_female 1910 2030 Input subjid8 pat_male 2020 2030 Input subjid9 pat_male 2020 2030 Input subjid10 pat_male 1910 2030 Input subjid11 pat_female 2020 2030 Input subjid12 pat_female 20202030 DefaultVariable score1 In this section, I want to implement partial regression analysis(i.e. score1 and score2) by controling the age,edu and sex. Here is my contrast for score1: 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 Here is my contrast for score2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.25 0.25 0.25 0.25 Any reply will be highly appreciated. Thanks. All the best. 2013-12-17 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] A prblem of tksufer tool
Hi Huang, I have similar question with you. In my case, I cannot visualizing inflated image by tksurfer but freeview. Looking forward to someone's help. All the best. 2013-12-14 Rujing Zha 发件人：Xiaojun.Huang lvdo...@gmail.com 发送时间：2013-12-14 20:44 主题：[Freesurfer] A prblem of tksufer tool 收件人：FreesurferFreesurfer@nmr.mgh.harvard.edu 抄送： Hi, I am processing the 3D PD patients brain now . After recon-all running, when I use the TKSurfer Tool to review the 3D brain, it is reverse and mistake the left and right. I test some other data and realized it may be something wrong with the Tksufer installing.How can I fix it? Thanks, Huang. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] segmentation incorrectly after recon-all
Hi Bruce, I upload the sugject lilei to your e-mail which is the segmentation incorrectly in -surfs. Thanks for your helping check it. All the best. 2013-12-14 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-14 05:27 主题：Re: [Freesurfer] segmentation incorrectly after recon-all 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu I guess you should upload the subject and we will take a look On Fri, 13 Dec 2013, Rujing Zha wrote: Hi Bruce, Here is my -aseg pitcutre in the attachment. The Sgmtn lable is Right-choroid-plexus. It is my understand that the aseg looks fine. Bruce, can you tell me how to fix the -surfs? Thanks in advance. All the best. 2013-12-13 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-13 20:48 主题：Re: [Freesurfer] segmentation incorrectly after recon-all 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Is that ventricle? Check the aseg and correct it if needed Cheers Bruce On Dec 13, 2013, at 3:12 AM, Rujing Zhacharujing...@163.com wrote: Dear all, How can I fix the false segmentation in the attachment. Thanks. All the best. 2013-12-13 Rujing Zha QQ图片20131213160952.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 从网易Rujing Zha邮箱发来的超大附件 lilei.zip (281.9 MB, 2014-01-13 09:19 到期) 下载 从网易Rujing Zha邮箱发来的超大附件 lilei.zip(281.9 MB,2014-01-13 09:19到期) 下载:http://fs.163.com/fs/display/?p=X-NETEASE-HUGE-ATTACHMENTfile=d8HDWxZCSvF1VHPLHFbWf2wlCyZh4CKVjBYazxgjhqx2M3FEZs3lL6ftzWZaEyzWpYanSnIHodlYfANe0P-B6A___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] after editing pial boundary in tkmedit
Hi Doug and Bruce, I have run recon-all -autorecon-pial -s my_subject after editing the pial by tkmedit. I donot know wether -autorecon-pial option running the process stages 24-31. So I want to know wether I need run -autorecon3 option as I run -autorecon-pial not -autorecon2-pial previously. Can I ensure 24-31 steps being done by running the recon-all -autorecon3 -s my_subject. GM thickness group analysis should be done correctly. Thanks. All the best. 2013-12-12 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] after PialEdit_tktools
Dear all, Can I just type recon-all -autorecon-pial -autorecon3 -s subjects after editing the pial by PialEdit_tktools? All the best 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Rujing Zha zh...@mail.ustc.edu.cn 发送时间：2013-12-10 12:03 主题：[Freesurfer] after PialEdit_tktools 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] after PialEdit_tktools
Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the -autorecon-pial option -autorecon2-pial option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] after PialEdit_tktools
Dear Bruce, Thanks. I see. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:29 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu sorry, looking at the script, I think: recon-all -autorecon-pial -s subject name should be all you need, but perhaps someone else can confirm. Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the -autorecon-pial option -autorecon2-pial option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人：Rujing Zhazh...@mail.ustc.edu.cn 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote: Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon- all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 _ ___ Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] part of GM missing
Dear all, In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to know how to paint the voxels to lable it as GM. And then run recon-all in a specific style to reconstruct the surfs. Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] part of GM missing
Dear all, What I mean is the boundary of pial is incorrect when I check that by this tkmedit subject brainmask.mgz -surfs I want to know how to change the boundary of the pial. Thanks. All the best. 2013-12-11 Rujing Zha 发件人：Rujing Zha zh...@mail.ustc.edu.cn 发送时间：2013-12-10 22:51 主题：[Freesurfer] part of GM missing 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear all, In tkmedit brainmask.mgz -surfs, there are a bit of GM part missing. I want to know how to paint the voxels to lable it as GM. And then run recon-all in a specific style to reconstruct the surfs. Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] after PialEdit_tktools
Dear all, I run recon-all -autorecon-pial -s subjects after editing the pial by PialEdit_tktools. However I only find -autorecon2-pial option in recon-all manual. So I donot know whether I should run the recon-all -s subjects -autorecon3 to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] R: Re: R: Re: R: Re: Linear regression
Dear Stefano, OK, I see. Thanks for your help. All the best. 2013-12-06 Rujing Zha 发件人：std...@virgilio.it 发送时间：2013-12-05 22:34 主题：R: Re: [Freesurfer] R: Re: R: Re: Linear regression 收件人：charujing123charujing...@163.com,freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Rujing, After recon-all and qcache, for correlation analysis, I have performed qdec by using a matrix that contains NPS test, 3 nuisance factors and one groups. For groups analysis I have applied mri_glmfit as described in the guide. Nothing in particular. Stefano Messaggio originale Da: charujing...@163.com Data: 5-dic-2013 2.15 A: stdp82std...@virgilio.it, freesurferfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: Linear regression Dear Stefano, I also want to make a correlation analysis between thickness and behavior data. Would you please send me your precious scripts for group analysis( unpaired t-test and correlation analysis) after recon-all? I want to study it if I get your permission. Thanks. All the best. 2013-12-05 Rujing Zha 发件人：std...@virgilio.it 发送时间：2013-12-05 02:06 主题：[Freesurfer] R: Re: R: Re: Linear regression 收件人：grevegr...@nmr.mgh.harvard.edu,freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Douglas, thank you very much for you kind reply. In the paper I have 3 groups (2 diseases and 1 controls). I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically significant regions where NPS test scores and thickness were correlated. 3 nuisance factors was also added to regressor. All results were corrected for multiple comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation. qdec analysis results have individuated a composite region (superior parietal cortex and precuneus) where NPS correlated with thinning. Now, if I understand, I should extract the mean thickness from superior parietal cortex and precuneus and I should perform a linear regression (and partial correlation) with an other statistical program (SPSS for example). Is there a better way to perform a regression the most possible similar to qdec computation? Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 4-dic-2013 17.35 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Linear regression On 12/02/2013 03:14 PM, std...@virgilio.it wrote: Tank you very much. A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? Finally a linear regression is done between cortical thickness of a composite region and NPS. However the authors discuss every individual region as related to disease. So a table with partials correlations of individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a composite region. Did you average the thickness over that region and then do the regression with NPS? B- I'd like to obtain the covariance matrix of the regression made between cortical thickness, group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? I cite the referee: The authors must provide the covariance matrix of the regression made between cortical thickness, group and covariates as supplementary information in order to increase the value of the results. Sorry, I don't understand what the reviewer is asking for. doug I don't have Matlab for mri_glmfit_pcc matlab. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 2-dic-2013 20.47 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Linear regression On 12/02/2013 02:22 PM, std...@virgilio.it wrote: Hi list, I have some questions, please. I performed linear regression by qdec to find the regions where the cortical thinning correlates with neuropsychological test (NPS), taking in account 3 nuisance factors. A- I individuated some posterior regions and now I'd like to build a table with partials correlations of individuals ROIs with NPS. How can I obtain the values for each region? Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? You can get PCC maps using the mri_glmfit_pcc matlab command. You can then do the averaging over region using mri_segstats. B- I'd like to obtain the covariance matrix of the regression made between cortical thickness,group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? C- Is there a specific reference for qdec? No, it is just a GLM so any GLM reference will do. Thank you very much, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N
Re: [Freesurfer] R: Re: R: Re: Linear regression
Dear Stefano, I also want to make a correlation analysis between thickness and behavior data. Would you please send me your precious scripts for group analysis( unpaired t-test and correlation analysis) after recon-all? I want to study it if I get your permission. Thanks. All the best. 2013-12-05 Rujing Zha 发件人：std...@virgilio.it 发送时间：2013-12-05 02:06 主题：[Freesurfer] R: Re: R: Re: Linear regression 收件人：grevegr...@nmr.mgh.harvard.edu,freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Douglas, thank you very much for you kind reply. In the paper I have 3 groups (2 diseases and 1 controls). I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically significant regions where NPS test scores and thickness were correlated. 3 nuisance factors was also added to regressor. All results were corrected for multiple comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation. qdec analysis results have individuated a composite region (superior parietal cortex and precuneus) where NPS correlated with thinning. Now, if I understand, I should extract the mean thickness from superior parietal cortex and precuneus and I should perform a linear regression (and partial correlation) with an other statistical program (SPSS for example). Is there a better way to perform a regression the most possible similar to qdec computation? Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 4-dic-2013 17.35 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Linear regression On 12/02/2013 03:14 PM, std...@virgilio.it wrote: Tank you very much. A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? Finally a linear regression is done between cortical thickness of a composite region and NPS. However the authors discuss every individual region as related to disease. So a table with partials correlations of individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a composite region. Did you average the thickness over that region and then do the regression with NPS? B- I'd like to obtain the covariance matrix of the regression made between cortical thickness, group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? I cite the referee: The authors must provide the covariance matrix of the regression made between cortical thickness, group and covariates as supplementary information in order to increase the value of the results. Sorry, I don't understand what the reviewer is asking for. doug I don't have Matlab for mri_glmfit_pcc matlab. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 2-dic-2013 20.47 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Linear regression On 12/02/2013 02:22 PM, std...@virgilio.it wrote: Hi list, I have some questions, please. I performed linear regression by qdec to find the regions where the cortical thinning correlates with neuropsychological test (NPS), taking in account 3 nuisance factors. A- I individuated some posterior regions and now I'd like to build a table with partials correlations of individuals ROIs with NPS. How can I obtain the values for each region? Do you mean the partial correlation coeff (PCC) at each voxel averaged over region? You can get PCC maps using the mri_glmfit_pcc matlab command. You can then do the averaging over region using mri_segstats. B- I'd like to obtain the covariance matrix of the regression made between cortical thickness,group and covariates. How can I do it? I'm not sure what you mean. Would this be a different matrix for each vertex? C- Is there a specific reference for qdec? No, it is just a GLM so any GLM reference will do. Thank you very much, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine
[Freesurfer] view inflated surfer by tksurfer
Dear all, After recon-all, I want to view the inflated volume by tksurfer subject rh inflated , but there is nothing in Display Window. I checked the file does exist in the surf directory. That is why? Thanks. All the best. 2013-12-03 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] delete skull part in GM by tkmedit
Dear Gabriel, I read the PialEdits_tktools, but I want to know whether it will determine surrounding voxels belonging to skull regions based on the voxels I have signed by brush? If it does, that is what I need. Thanks. All the best. 2013-12-03 Rujing Zha 发件人：Gabriel Gonzalez Escamilla ggon...@upo.es 发送时间：2013-12-03 20:17 主题：Re: [Freesurfer] delete skull part in GM by tkmedit 收件人：Rujing Zhacharujing...@163.com 抄送： Rujing, Have you tryed the tutorial? http://freesurfer.net/fswiki/FsTutorial/PialEdits_tktools You just need to edit the brain mask and then run again some parts of the recon-all Bests, Gabriel - Mensaje original - De: Rujing Zha charujing...@163.com Fecha: Martes, 3 de Diciembre de 2013, 8:46 am Asunto: [Freesurfer] delete skull part in GM by tkmedit A: freesurfer freesurfer@nmr.mgh.harvard.edu Dear all, I have read the troubleshooting in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I want to know if thereis a similar method to remove skull part in GM? I donot want to use -gcut and watershed option. I think control point method is better than -gcut option in my case. Thanks, All the best. 2013-12-03 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] delete skull part in GM by tkmedit
Dear Bruce, Here is my opinion about the better option control points in my case. In control points, I think it is several voxels signed by myself that freesurfer tools will consider these voxels as white matter and freesurfer tools will compare these voxels and surrounding voxels to recognise whether surrounding voxels belong to white matter. I think the thought is excellent. In skull stripping, the brainmask volume will lose part of cerebellum if I lower watershed threshold. If manually erase part of skull, does freesurfer tool will also consider surrounding voxels (just the same as control points, but in this case for erasing skull ) to automatically erase other voxels which is actually belonging to skull regions but I didnot erase them? If it does, that is very nice. Anyway I think combine manually control some points and freesurfer tools automatically segmentation will generate a beautiful result. Thanks. All the best. 2013-12-03 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-03 21:25 主题：Re: [Freesurfer] delete skull part in GM by tkmedit 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing why do you think control points will help in your case, where a tiny bit of skull is grabbed by the pial surface? I think changing the skull stripping or just manually erasing that bit are your best options. cheers Bruce On Tue, 3 Dec 2013, Rujing Zha wrote: Dear all, I have read the troubleshooting in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I want to know if thereis a similar method to remove skull part in GM? I donot want to use -gcut and watershed option. I think control point method is better than -gcut option in my case. Thanks, All the best. 2013-12-03 Rujing Zha The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] view inflated surfer by tksurfer
Dear Bruce, I should have hit mris_info. My server has 24 CPUs and 64G RAM. I tried the redraw key, but there was a little bit gray scale image. Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-03 22:10 主题：Re: [Freesurfer] view inflated surfer by tksurfer 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu I meant mris_info not mri_info. What is your hardware environment? Are you connecting over ssh or something? I guess the simplest thing to try is clicking the redraw key in tksurfer after it comes up On Tue, 3 Dec 2013, Rujing Zha wrote: Dear Bruce, Thanks for your help. The size is about 4MB. I am so sorry about poor understanding what you said mri_info, but I attach the command line message in the attachment. I can see that in freeview. Thanks. All the best. 2013-12-03 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-12-03 21:26 主题：Re: [Freesurfer] view inflated surfer by tksurfer 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu what is the size of the file? What does mris_info tell you about it? Can you view it in freeview with freeview -f $SUBJECTS_DIR/$subject/surf/rh.inflated then change to 3D viewing? On Tue, 3 Dec 2013, Rujing Zha wrote: Dear all, After recon-all, I want to view the inflated volume by tksurfer subject rh inflated , but there is nothing in Display Window. I checked the file does exist i n the surf directory. That is why? Thanks. All the best. 2013-12-03 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
Dear Louis, Thanks for your helpful suggestions. I will try. All the best. 2013-12-04 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 23:13 主题：Re: Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, If portions of gray matter have been removed, then that will need to be corrected. You can definitely remove skull/dura manually from the brainmask.mgz volume (see link below), but that can be time-consuming and may not be necessary. It's hard to know for sure if a brainmask.mgz is bad until you have generated the surfaces or have some experience with similar cases processed with Freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Tue, 3 Dec 2013, Rujing Zha wrote: Dear Louis, Thanks for your helpful prompt in advance. I see. In my case, there is a not properly stripping, there is a not properly gray matter(there are a some skull considered as gray matter). Did you mean I can draw the segmentation without considering the skull stripping? And a bad brainmask.mgz will not influence the GM thickness analysis? Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 03:58 主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, Even if there is some skull/dura left after the skullstrip step in recon-all, it still may not negatively impact the surfaces. It might be worth running the remaining recon-all steps to see how the surfaces turn out. If you want to swap-in a better skullstripped volume into the recon-all stream then you just need to replace the brainmask.mgz and continue with autorecon2 and autorecon3. Keep in mind that the new brainmask.mgz volume still needs to be in the conformed anatomical space, so use the T1.mgz or brainmask.mgz to create the improved skullstrip volume which will replace the existing brainmask.mgz. -Louis On Mon, 2 Dec 2013, Rujing Zha wrote: Dear all, Part of subjects 3d images cannot be stripped skull and neck properly in ?? ? recon-all default. I have got the brain volume mask, how I can using the ?? ? existing proper mask to help strip skull in recon-all and next workflow? ?? ? Thanks.Any reply will be appreciated. All the best. 2013-12-02 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all strip skull and neck by brain volume mask
Dear all, Part of subjects 3d images cannot be stripped skull and neck properly in recon-all default. I have got the brain volume mask, how I can using the existing proper mask to help strip skull in recon-all and next workflow? Thanks.Any reply will be appreciated. All the best. 2013-12-02 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] viewing slices dynamically by tkmedit
Hi Louis, Thanks for your helpful suggestion. Maybe I just click the slice -/+ module if I want to view all the slices of one subject's volume in tkmedit. But I do not want to click the button continuously to view all the slices. I want to press a button/key once, then I can see all the slices one by one in a volume automatically; the automatically view will halt if I press a button/key again or other button/key. Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 03:50 主题：Re: [Freesurfer] viewing slices dynamically by tkmedit 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, You can use a tcl script to take several snapshots in tkmedit, then you could use the convert command (part of ImageMagick distro) or something similar to create an animated gif. With the convert command you would use the -adjoin and -delay flags. You could use one of the tcl scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). You could also get multiple snapshots with freeview using command line flags and a shell script. -Louis On Sat, 30 Nov 2013, Rujing Zha wrote: Dear all, I want to see the slices as a shape of movie in tkmedit. Do anyone can tell me how to do it? Thanks. All the best. 2013-11-30 Rujing Zha The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
Dear Louis, Thanks for your helpful prompt in advance. I see. In my case, there is a not properly stripping, there is a not properly gray matter(there are a some skull considered as gray matter). Did you mean I can draw the segmentation without considering the skull stripping? And a bad brainmask.mgz will not influence the GM thickness analysis? Thanks in advance. All the best. 2013-12-03 Rujing Zha 发件人：Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu 发送时间：2013-12-03 03:58 主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, Even if there is some skull/dura left after the skullstrip step in recon-all, it still may not negatively impact the surfaces. It might be worth running the remaining recon-all steps to see how the surfaces turn out. If you want to swap-in a better skullstripped volume into the recon-all stream then you just need to replace the brainmask.mgz and continue with autorecon2 and autorecon3. Keep in mind that the new brainmask.mgz volume still needs to be in the conformed anatomical space, so use the T1.mgz or brainmask.mgz to create the improved skullstrip volume which will replace the existing brainmask.mgz. -Louis On Mon, 2 Dec 2013, Rujing Zha wrote: Dear all, Part of subjects 3d images cannot be stripped skull and neck properly in recon-all default. I have got the brain volume mask, how I can using the existing proper mask to help strip skull in recon-all and next workflow? Thanks.Any reply will be appreciated. All the best. 2013-12-02 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] delete skull part in GM by tkmedit
Dear all, I have read the troubleshooting in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I want to know if thereis a similar method to remove skull part in GM? I donot want to use -gcut and watershed option. I think control point method is better than -gcut option in my case. Thanks, All the best. 2013-12-03 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] viewing slices dynamically by tkmedit
Dear all, I want to see the slices as a shape of movie in tkmedit. Do anyone can tell me how to do it? Thanks. All the best. 2013-11-30 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] nii format input for recon-all
Dear all, I have done the recon-all for DICOM format input of all subjects. Part of subjects extracted brain volume not very perfectly. I want to use brain volumes nifti format which have strip the skull and neck well. My question is how to use the brain volume in nii format to segment and next recon-all analysis. Thanks. All the best. 2013-11-29 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs
Dear Anita, Would you please tell me where I can find Cortical Thickness of a volume-defined ROI? Thanks, All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 21:51 主题：[Freesurfer] Cortical thickness/surface area in volume-defined ROIs 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs
Dear, I get it. Thanks. All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 22:18 主题：Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups
Dear freesurfer experts, I met a question about how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups. Thanks. All the best. 2013-11-25 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups
Dear professor Bruce, Thanks for your attention. After recon-all, I get the cortex thickness of all subjects. Then I check the segmentations by tkmedit your_subject_name brainmask.mgz -surfs -aseg. However, my fundamental knowledge is so little that I donot know whether the quality of segmented data I can use in further analysis. That is to say, I donot know whether 3d structure of subjects is appropriate in further cortex thickness analysis. Thanks, All the best. 2013-11-25 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-25 22:23 主题：Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, sorry, I don't understand. Can you clarify what you are trying to do? Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: Dear freesurfer experts, I met a question about how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups. Thanks. All the best. 2013-11-25 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups
Dear professor Bruce, Thanks for your precious reply. I will try. All the best. 2013-11-26 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-25 23:20 主题：Re: [Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu I see. There is really nothing to do but visually inspect them for accuracy. Sorry, you will need to educate yourself a bit on what the anatomy looks like to tell if the boundaries are accurate. It's really not that difficult once you get a bit of experience. Feel free to send us images that you have questions about if you want. cheers Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: Dear professor Bruce, Thanks for your attention. After recon-all, I get the cortex thickness of all subjects. Then I check the segmentations by * tkmedit your_subject_name brainmask.mgz -surfs -aseg. However, my fundamental knowledge is so little that I donot know whether the quality of segmented data I can use in further analysis. That is to say, I donot know whether 3d structure of subjects is appropriate in further cortex thickness analysis. Thanks, All the best. 2013-11-25 Rujing Zha Bruce Fischl fis...@nmr.mgh.harvard.edu ?2013-11-25 22:23 ???Re:[Freesurfer] how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 groups Rujing Zhacharujing...@163.com ???freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing, sorry, I don't understand. Can you clarify what you are trying to do? Bruce On Mon, 25 Nov 2013, Rujing Zha wrote: Dear freesurfer experts, I met a question about how to decide objectively whether I can use the segmented data of one subkects to analyze cortex thickness between 2 grou ps. Thanks. All the best. 2013-11-25 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all Process Flow
Dear Bruce, Thanks for your precious promt. All the best. 2013-11-22 Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-21 22:42 主题：Re: [Freesurfer] recon-all Process Flow 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing sure, you can run them individually if you want. Just make sure it is in the right order and you don't skip any or they will fail cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, As we know, recon-all is a integrated code. I have read this code process flow in the website http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I run the a series of command which are presented in command line step by step to realize all the function of recon-all? All the best. 2013-11-21 Rujing Zha Rujing Zhacharujing...@163.com ?2013-11-21 22:30 ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination freesurferfreesurfer@nmr.mgh.harvard.edu ??? Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha Bruce Fischl fis...@nmr.mgh.harvard.edu ?2013-11-21 21:39 ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination Rujing Zhacharujing...@163.com ???freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly with out deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-a ll again? All the best. 2013-11-21 _ ___ Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all -s subjects -all unexpected termination
Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-21 21:39 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all Process Flow
Dear all, As we know, recon-all is a integrated code. I have read this code process flow in the website http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I run the a series of command which are presented in command line step by step to realize all the function of recon-all? All the best. 2013-11-21 Rujing Zha 发件人：Rujing Zhacharujing...@163.com 发送时间：2013-11-21 22:30 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-21 21:39 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all -s subjects -all unexpected termination
Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to obtain subjects cortical thickness and then analyze unpair t-test
Dear all, Ater recon-all,which image can I select to group t-test? And do they need process in advance? Thanks very much. All the best. 2013-11-19 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to obtain subjects cortical thickness and then analyze unpair t-test
Dear doug, Thanks for your precious prompt, I will try. All the best. 2013-11-20 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-11-20 00:20 主题：Re: [Freesurfer] how to obtain subjects cortical thickness and then analyze unpair t-test 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Look at our tutorial on group analysis on the wiki. Briefly, you need to run mris_preproc (transforms all subjects' thickness maps to surface atlas space), mri_surf2surf to smooth the thickness maps, then create an FSGD file and run mri_glmfit to perform the t tests doug On 11/19/2013 08:07 AM, Rujing Zha wrote: Dear all, Ater recon-all,which image can I select to group t-test? And do they need process in advance? Thanks very much. All the best. 2013-11-19 /Rujing Zha/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer5.3 version In CentOS5
Dear all, In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be compatible? Thanks! All the best. 2013-11-15 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz doesnot have mri_strip_skull codes
Dear FreeSurfer Users, I downloaded FreeSurfer latest version in this website:ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz. I want to strip 3d structure skull by mri_strp_skull,but this package does not have this codes.Why? What else can I do? Thanks! Any reply and advice will be appreciated! Best. 2013-10-28 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
